If you start during the event end end after it, you don't get extra bonus poits.
If you start before the event, complete it in the bonus event, you get extra bonus poits.
Bone1970 & Bone trader don't believe in a no-win senario, Kirk's protege. Fed Tac's. BNE Fed Sci.
Bag of Bones & Bone Ugly don't believe in a no-win senario, Kirk's protege. Rom/Fed Tac. Bone & Bone2 don't believe in a no-win senario, Kirk's protege. KDF Eng's.
Warning: Not a native English-speaker, sorry if my English sucks.
Basically, if you're within the Bonus Marks time period when marks are awarded to you, you'll get the bonus for that Mark drop.
So if you complete waves 1 & 2 of a Fleet Alert at a minute before the start and then complete the rest of it after the Bonus event starts, you'll get bonus marks for waves 3, 4 and the overall completion, but not for waves 1 & 2, because the game awarded marks for those waves outside the Bonus Mark event.
If you're doing Tau Dewa Sector patrol for example, wait until bonus marks event to turn it in.
You'll get 75 instead of 60 Romulan marks, no matter when you completed it.
What matters in this case is the time you turn it in.
That doesn't apply to boxes with marks, as far as I know, though. It counts when you got the box, not when you open it.